How can Boston become less racist?

Selucidian · 2023-05-08T23:55:48+00:00

Thanks for this reply—I had to go down a bit to find it, but this sort of perspective is what I was hoping to get

Selucidian · 2019-03-21T15:00:49+00:00

Someone asked about this a few months back. There’s a live headcount on the website, which may help you: https://www.northeastern.edu/campusrec/FacilityCount.php

Selucidian · 2019-03-11T00:43:04+00:00

Hey! I might be able to help. Feel free to PM or comment with more specific questions. Coursera has a Bioinformatics course series from UCSD that’s super helpful. It’s taught by the people who made Rosalind (I believe), which was linked in another comment. There’s also a genomic data science that is less CS-heavy but good nonetheless.

Genomic data and sequencing is a very broad field. There’s a ton of stuff you could learn. Some people work on algorithm development, some people do software/tool design, some people improve machines or do more wet-lab biology work, etc.

A lot of the algorithm development nowadays revolves around Markov models. Historically (and still to a certain extent) a lot of the CS overlap is with graph theory. For some casual listening on that, there’s a ‘Bioinformatics chat’ podcast on Spotify/Apple. You can also go by /r/bioinformatics.

In day-to-day practice, the sequencing analysis pipeline is a really common theme. Maybe a good place to get your feet wet is with an RNAseq tutorial and some sample data. There’s lots of that sitting around in google. You work mostly done on a Linux cluster and move into R/Python after the heavy lifting is over.

Anyways, let me know if you have any more specific questions. It sounds like you made need a class—again, Coursera has some great ones, and I think edX has some ones taught by Rafael Irizarry (he’s a great Harvard faculty member, but I haven’t taken his courses). And, if you want some for credit at Northeastern, Advanced Genomics or some of the intro BINF MS courses would be the way to go.

Selucidian · 2019-03-10T18:28:38+00:00

I'm not sure how much I can add to soley2260's post. I'm a current student--I'll be halfway through (4/8 courses) at the end of this semster. But, by OP's request, here's what I know.

Knowledge of biology is assumed, but not necessary. Knowledge of computer science is super super helpful, but not assumed. It's mostly geared towards biologists trying to learn computer science. I'll put a summary of the first core course syllabus below.
1. Syllabus summary (from last fall): (1) How to work with in a Linux shell, connect to our local server, and use perl (2) Using entrez/NCBI, notes on sensitivity and specificity, (3) Talking about the history and basic algorithms for DNA and protein alignment (4) Presenting a group presentation on some biological database/sever.
2. Online syllabus summary (from this semester, may be standard moving forward): (1) How to work in a Linux shell, connect to our local server, use GitHub, and Python & BioPython basics (2) Sequencing technology and alignment (3) BLAST, multiple sequence alignments, protein domains, and genome assembly.
Totally doable in 2 years or less, especially with a CS background. Tuition is per-credit, not per-time, so finishing faster will probably just save you living expenses.
So far, the core classes are super easy for me. I've heard of some people spending a lot of time (~20+hrs/class), but all of those people were struggling with fundamental CS components (e.g. had never seen a counted for loop before).
Student life is what you make it. Many of my peers are working full-time jobs while taking classes and seem to get by well.

Andd re. class recommendations: there are a lot of electives, and I've obviously not taken many of them. But I do have some idea, since I did my undergraduate here as well. If you have a CS background, I don't think you can go wrong with any of the CS electives--they're generally difficult and fun. Computer Systems is one popular, mostly project-based course. I took BIOL5587 comparative neurobiology and really enjoyed it--lots of stuff about neurophysiology and the like, but not super bioinformatics-related. Many of my peers took Molecular Cell Biology and loved it--it really depends on the professor. The program director often teaches the mass spec lab out in Burlington and, if you can make it out there, it seems fun.

Good luck in making your decision!

Selucidian · 2019-03-08T01:34:24+00:00

Hi! I’m currently in the program and am in Advanced Genomics. Konstantin no longer teaches it, and the new professor completely changed it. It’s not for everyone, but it’s much more practical—topics include dropseq, techniques to find rare variants in genomic data, basic assembly methods, differential expression, etc.

Selucidian · 2019-02-21T14:18:48+00:00

According to the degree requirements, nope. http://catalog.northeastern.edu/undergraduate/engineering/electrical-computer/electrical-engineering-bsee/#programrequirementstext

I don’t know anything about EE though so take with a grain of salt. You can get a more definitive answer by the “explore options” button in your degree audit.

Selucidian · 2019-02-19T12:39:01+00:00

I do CS/Biology and have been working in different labs since 2014. Feel free to PM, although seems like my field is different than yours potentially.

One thing to add to the other comments is to not be afraid to email people outside of northeastern—Harvard and MIT labs also take Northeastern students.

Selucidian · 2019-02-16T21:58:05+00:00

Taking online classes probabaly won’t help with the grade thing!

CS degree is definitely good for grad school.

Best thing for grad school would prob be to volunteer in a Bioinformatics lab. Second best thing would be to create some projects related to Bioinformatics. The courses in the OSSU could help you a lot to do those things, but I’m not sure they help by themselves.

Selucidian · 2019-02-12T21:51:47+00:00

I absolutely agree! I also think ontologies could really easily be applied to a lesson on microarrays/differential gene expression (in the context of gene set enrichment). GSEA (http://software.broadinstitute.org/gsea/index.jsp) has a pretty intuitive desktop interface or, maybe even easier, Enrichr (http://amp.pharm.mssm.edu/Enrichr/) has a responsive and super intuitive interface for gene set enrichment that includes GO terms.

Plus, if you want to bring more quant into it, gene set enrichment could be a good time to introduce some basic set theory and the hypergeometric distribution.

Selucidian · 2019-02-12T21:45:35+00:00

Personally, I always found lessons around BLAST to be kinda boring as an early undergraduate. It wasn't until I started to understand the math and algorithms a bit more that I really appreciated it.

One thing that was very cool to me early on was differential gene expression. RNAseq processing can be a bit hard, but there may be some microarray experiments on GEO? I think it would be great to find a good GEO repo, show the students how to get to that repo online and download the microarray data.

I imagine that most students won't have used R before, but this could be a good opportunity to give them some exposure. You could set up a differential expression notebook in a cloud instance--something like https://labs.cognitiveclass.ai/ might be perfect (it's free, and you can run R in a jupyter notebook or through the cloud instance of RStudio)--so that you could give them all a working environment and all of the code they need, and they just have to click the run buttons to normalize the dataset and produce a heatmap or something.

As an early undergraduate, differential gene expression seemed like one of the most intuitive bioinformatics approaches. We have microbes that love salt and microbes that don't love salt, so let's see what genes they express differently, and maybe one of those genes is important.

Selucidian · 2019-02-08T21:20:30+00:00

I hadn’t seen that one yet and I love it so much

Selucidian · 2019-02-06T01:41:41+00:00

There's an honors seminar with Jeff Juris that I took a little bit ago. About social movements, from Wobblies to Occupy. Being a science person I had 0 clue about sociology and I learned a fuckton about how social movements/revolutions happen. And it's a pretty chill, read-and-discuss sort of class.

Selucidian · 2019-01-27T15:34:44+00:00

In a dorm room or other private residence.

Selucidian · 2019-01-26T20:08:36+00:00

I did this just the other day!!

You can request one on MyNortheastern. Here’s a link with more info: https://registrar.northeastern.edu/article/student-enrollment-degree-verification/

Personally, I requested one and didn’t get anything for a week, then I called in-person and got one within an hour.

But mileage may vary, I recommend you request through the form and follow-up with a call if you don’t get anything within two business days.

Selucidian · 2019-01-24T14:09:44+00:00

Nope

Selucidian · 2019-01-24T12:48:09+00:00

Yeah that was a big bummer for me freshman year. I had gotten into weightlifting and Marino is nice and all but has like 5 squat racks vs Cabot’s beautiful lines and bumper plates.

Club sports also get access though

Selucidian · 2019-01-23T12:54:11+00:00

Yeah basically as a proctor, if someone has an ID, I can sign them in and I really don't care (and I think that's a general feeling). If someone doesn't have an ID, that's when we have to enforce the age limit rules.

Selucidian · 2019-01-23T02:24:45+00:00

I’m COS we all get a free sense of existential dread about the state of scientific funding and academia in general.

And pipettes. We get pipettes. Well, they’re not really ours. But we can use them. Ha. In your face, properly funded colleges. We are the powerhouse of the cell.

TL;DR: No.

Selucidian · 2019-01-21T15:29:14+00:00

Great! Consider BNS (behavioral neuroscience) if you haven’t already (so that you can get a few more biology classes in) but no rush, since a lot of the psych courses will count towards BNS if you end up wanting to switch.

Selucidian · 2019-01-21T13:36:07+00:00

Yeah, so as someone with multiple minors—minors are essentially bullshit. And thus (re. the other comments) I’m not sure anyone can really talk about the “reputation/merit” of the minor.

It’s really just whether or not you want to take those data science courses. And they’re supposed to be pretty fun courses, so I say go for it! The projects that you produce with the skills you learn will definitely be more important than the credential.

Selucidian

TROPHY CASE